I'm excited to have a book chapter on PyRx published in a book from Springer Publishing titled “Chemical Biology – Methods and Protocols”. I'm very thankful to editors for the opportunity to publish this work and they did a great job in compiling and editing this book. See the Table of Contents that includes many interesting methods and protocols used in modern Chemical Biology. In particular, Small-Molecule Library Screening by Docking with PyRx describes utilization of this essential software tool for the field of chemical biology and highlights key considerations and strategies for performing molecular docking.... read more
This is a brief introduction to PyRx workspace. It shows where PyRx stores different files and how to create a new workspace.
We are excited to have new Mac OS X installer available for download. PyRx sells have been good for the past two years, and we thank each and very customer. Your support is much appreciated. Your contributions is what makes it possible to create PyRx installers.
We had 6,299 downloads in 2013 for the free version of PyRx hosted on SourceForge. The table below shows number of downloads broken down by operating system. SourceForge provides excellent tools for download statistics and this table was copied from here. Thank you all for using PyRx.... read more
We are pleased to announce the release of PyRx 0.9.2. One of the main new feature implemented in PyRx 0.9.2 is an option to execute AutoDock 4 or Vina using remote execution mode as shown in the image below. This is a great feature for users who want to run docking on a remote cluster without using CPU cycles of their Desktops.
PyRx 0.9 and 0.9.1 users, please use PyRx > Help > Check for Updates... menu to update to this version. The following are new features and bug fixes implemented in 0.9.2 release:... read more
To make protein side chains flexible during the docking, please load the molecule in PyRx using File > Load Molecule and click on + sign next to the molecule in Navigator > Molecules panel to see the list of residues. Then using Shift or Control keys, select residues you wish to make flexible. You can click on Toggle Selection Sphares icon on the main toolbar (the last icon with pink highlights) to see selected residues in 3D Scene. Then with residues selected under Navigator > Molecules panel, right click and select AutoDock > Flexible Residues menu as shown in the image below. This creates _flex folder under _Navigator > AutoDock > Macromolecules _panel. Select this _flex folder in Select Molecules tab when using Vina or AutoDock Wizard and PyRx would automatically prepare and run flexible docking with Vina or AutoDock respectively. Please note that making side chains flexible works only for small proteins with fewer than 200 residues. For larger proteins with more than 200 residues, PyRx might crash to guard against a stack overflow.... read more
We are pleased to announce the release of PyRx 0.9.1. This is a minor bugfix release. PyRx 0.9 users, please use PyRx > Help > Check for Updates... menu to update. The following is a new feature and a bug fix implemented for 0.9.1 release:
We are pleased to announce the release of PyRx 0.9. The following are new features and bug fixes implemented for 0.9 release:
 Vina Wizard is now using the number of CPUs (--cpu option). Please use Edit > Preferences and enter Available CPUs to specify this number. By default, PyRx sets it to the number of available CPUs minus one, or just one if there is only one CPU available.... read more
I wrote this small script that can be used to rotate molecules in PyRx. You can try it by downloading rotate.py and then use File → Run Python Script menu from PyRx to run it. To stop this rotation, click on Python Shell tab under Controls panel, type
stop() and hit Enter. The following is the complete code for rotate.py and it's intended for (Python) developers who want to learn how it's done.
def rotate(event): frame.mayaviEngine.scene.camera.azimuth(1); #change 1 to any other degree as needed. frame.mayaviEngine.scene.render() def stop(): frame.timer.Stop() del frame.timer import wx frame.Bind(wx.EVT_TIMER, rotate) frame.timer = wx.Timer(frame) frame.timer.Start(50) #you change the rate here ... [read more](/p/pyrx/news/2012/03/rotating-mayavi-camera/)
This post explains how to install NVIDIA proprietary drivers on CentOS 6. By default, CentOS 6 comes with nouveau drivers, which for 3D (OpenGL) rendering, is order of magnitude slower that NVIDIA's proprietary drivers. For instance, I had glxgear running at round 400 frames per second (FPS) before installing NVIDIA proprietary drivers and at around 1000 FPS after. So it pays to add this extra step to your CentOS 6 installation. Before we start, make sure you have all required packages installed:
yum groupinstall "Development Tools" yum install kernel-devel kernel-headers dkms ... [read more](/p/pyrx/news/2011/12/installing-nvidia-driver-on-centos-6/)
I started PyRx project 3 years ago in 2008 to fill an unmet need for a virtual screening GUI. There were many users who couldn't run virtual screening and there were no tools available. See for instance: ADL: virtual screening. Over the years, PyRx has gained many users. After I moved PyRx site to SourceForge its ranking jumped from below 300k to above 1k as shown in the image on the right. The estimated cost for PyRx is currently around $266k and it would require around 5 person-years to develop it from scratch. See http://www.ohloh.net/p/pyrx/estimated_cost for more info. If you take into account all the dependencies, these numbers are at least 100x higher.... read more
I'm very excited to participate in the iDEA Conference. I was bold enough to submit one of the 30 entries for the iDEA Challenge and was rewarded by having an opportunity to participate in this conference. Illumina is a leader in Next Generation Sequencing (NGS) technology and they have done a brilliant job organizing this event. In case you haven't heard, NGS is rapidly replacing DNA microarrays as a diagnostics (Dx) and scientific tool. In fact, many of the software companies that used to work on DNA microarrays are now working on NGS.... read more